#include <BDR.hh>
Public Member Functions | |
| BDR () | |
| default constructor More... | |
| BDR (BDR const &rval) | |
| copy constructor More... | |
| ~BDR () override | |
| default destructor More... | |
| MoverOP | clone () const override |
| clone this object More... | |
| MoverOP | fresh_instance () const override |
| create this type of object More... | |
| bool | use_fullmer () const |
| use full-mer fragments when building the loop? (default false) More... | |
| bool | use_sequence_bias () const |
| use sequence biased fragments when building the loop? (default false) More... | |
| Real | max_linear_chainbreak () const |
| the maximum allowed linear chainbreak (default 0.07) More... | |
| String const & | centroid_loop_mover_str () const |
| the loop mover string to use during centroid build (default "RemodelLoopMover") More... | |
| bool | redesign_loop_neighborhood () const |
| redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More... | |
| String const & | resfile () const |
| name of the resfile to use during design-refine; empty string implies no resfile More... | |
| core::Size | dr_cycles () const |
| the number of design-refine cycles to perform, default 3 More... | |
| ScoreFunction const & | centroid_scorefunction () const |
| the centroid level score function, default "remodel_cen" More... | |
| ScoreFunction const & | fullatom_scorefunction () const |
| the full-atom level score function, default score12 More... | |
| void | add_instruction (BuildInstructionOP bi, String const &aa_during_design_refine=String()) |
| add instruction to the manager of this BDR (no copy) More... | |
| void | create_directed_dependency (BuildInstructionOP u, BuildInstructionOP v) |
| create directed dependency between two instructions More... | |
| void | use_fullmer (bool const flag) |
| use full-mer fragments when building the loop? More... | |
| void | use_sequence_bias (bool const flag) |
| use sequence biased fragments when building the loop? (default false) More... | |
| void | max_linear_chainbreak (Real const threshold) |
| the maximum allowed linear chainbreak More... | |
| void | centroid_loop_mover_str (String const &loop_mover_str) |
| the loop mover string to use during centroid build More... | |
| void | redesign_loop_neighborhood (bool const flag) |
| redesign the neighborhood around the loop? if false, then just repacks during the design phase More... | |
| void | resfile (String const &filename) |
| name of the resfile to use during design-refine; empty string implies no resfile More... | |
| void | dr_cycles (core::Size const cycles) |
| set the number of design-refine cycles to perform More... | |
| void | centroid_scorefunction (ScoreFunction const &sfx) |
| set the centroid level score function More... | |
| void | centroid_scorefunction (ScoreFunctionOP sfx) |
| set the centroid level score function More... | |
| void | fullatom_scorefunction (ScoreFunction const &sfx) |
| set the full-atom level score function More... | |
| void | fullatom_scorefunction (ScoreFunctionOP sfx) |
| set the full-atom level score function More... | |
| void | apply (Pose &pose) override |
| apply defined moves to given Pose More... | |
| std::string | get_name () const override |
| Each derived class must specify its name. The class name. More... | |
 Public Member Functions inherited from protocols::moves::Mover | |
| Mover () | |
| virtual MoverOP | create () |
| MoverCOP | get_self_ptr () const |
| MoverOP | get_self_ptr () |
| MoverCAP | get_self_weak_ptr () const |
| MoverAP | get_self_weak_ptr () |
| Mover (std::string const &type_name) | |
| sets the type for a mover; name_ has been removed (2010/05/14) More... | |
| virtual void | test_move (Pose &pose) |
| : Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
| virtual bool | reinitialize_for_each_job () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
| virtual bool | reinitialize_for_new_input () const |
| Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
| MoverStatus | get_last_move_status () const |
| end parser interface, start Job Distributor interface///////////// More... | |
| void | reset_status () |
| resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
| virtual core::pose::PoseOP | get_additional_output () |
| Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
| void | set_type (std::string const &setting) |
| Set the 'type' string. More... | |
| std::string | get_type () const |
| void | type (const std::string &type_in) |
| Set the 'type' string. More... | |
| std::string const & | type () const |
| Get the set 'type' string. More... | |
| virtual void | set_input_pose (PoseCOP pose) |
| setter for poses contained for rms More... | |
| virtual void | set_native_pose (PoseCOP pose) |
| setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
| PoseCOP | get_input_pose () const |
| PoseCOP | get_native_pose () const |
| virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data) |
| Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
| void | set_current_job (protocols::jobdist::BasicJobCOP job) |
| jobdist::BasicJobCOP | get_current_job () const |
| virtual void | set_current_tag (std::string const &new_tag) |
| std::string | get_current_tag () const |
| A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
| virtual void | show (std::ostream &output=std::cout) const |
| Outputs details about the Mover, including current settings. More... | |
| virtual core::Real | last_proposal_density_ratio () |
| virtual void | clear_info () |
| Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
| virtual Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More... | |
Static Public Member Functions | |
| static String | neighborhood_calc_name () |
| the name for the loops' neighborhood calculator More... | |
| static String | loops_buns_polar_calc_name () |
| the name for the loops' buried unsatisfied polars calculator More... | |
| static String | neighborhood_buns_polar_calc_name () |
| the name for the loops' neighborhood buried unsatisfied polars calculator More... | |
| Static Public Member Functions inherited from protocols::moves::Mover | |
| static std::string | name () |
| static void | register_options () |
| Overload this static method if you access options within the mover. More... | |
Private Types | |
| typedef protocols::moves::Mover | Super |
Private Member Functions | |
| BDR & | operator= (BDR const &rval) |
| copy assignment More... | |
| bool | centroid_build (Pose &pose) |
| run the centroid level build stage More... | |
| bool | design_refine (Pose &pose) |
| run the design-refine stage More... | |
| TaskFactoryOP | generic_taskfactory () |
| return a TaskFactory useable as a starting point for either design or refinement More... | |
| void | process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf) |
| process a continuous design string, adding appropriate operations to the TaskFactory More... | |
| void | process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf) |
| process a design string containing an insert, adding appropriate operations to the TaskFactory More... | |
Static Private Member Functions | |
| static utility::vector1< bool > const & | allowed_surface_aa () |
| return a boolean vector specifying allowed a.a. when designing on the surface More... | |
Private Attributes | |
| BuildManager | manager_ |
| the BuildManager More... | |
| DesignInfo | design_info_ |
| Stores instructions' original interval and a string denoting the sequence during design. More... | |
| bool | use_fullmer_ |
| use full-mer fragments when building the loop? (default false) More... | |
| bool | use_sequence_bias_ |
| use sequence biased fragments when building the loop? (default false) More... | |
| Real | max_linear_chainbreak_ |
| the maximum allowed linear chainbreak (default 0.07) More... | |
| String | centroid_loop_mover_str_ |
| the loop mover string to use during centroid build (default "RemodelLoopMover") More... | |
| bool | redesign_loop_neighborhood_ |
| redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More... | |
| String | resfile_ |
| name of the resfile to use during design-refine; empty string implies no resfile More... | |
| core::Size | dr_cycles_ |
| the number of design-refine cycles to perform, default 3 More... | |
| ScoreFunctionOP | centroid_sfx_ |
| the centroid scorefunction to use, default "remodel_cen" More... | |
| ScoreFunctionOP | fullatom_sfx_ |
| the full-atom scorefunction to use, default score12 More... | |
| VarLengthBuildOP | vlb_ |
| VLB for centroid_build. More... | |
Additional Inherited Members | |
| Protected Member Functions inherited from protocols::moves::Mover | |
| void | set_last_move_status (MoverStatus status) |
| nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Member Typedef Documentation
◆ BuildInstructionOP
| typedef protocols::forge::build::BuildInstructionOP protocols::forge::components::BDR::BuildInstructionOP |
◆ BuildManager
◆ DesignInfo
| typedef utility::vector1< OriginalInterval2DesignString > protocols::forge::components::BDR::DesignInfo |
◆ Interval
◆ MoverOP
◆ Original2Modified
| typedef protocols::forge::build::BuildManager::Original2Modified protocols::forge::components::BDR::Original2Modified |
◆ OriginalInterval2DesignString
| typedef std::pair< Interval, String > protocols::forge::components::BDR::OriginalInterval2DesignString |
A pair storing a instruction's original interval and a string denoting the sequence during design.
- Remarks
- This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
◆ Pose
◆ Real
◆ ScoreFunction
◆ ScoreFunctionOP
◆ Size
◆ String
| typedef std::string protocols::forge::components::BDR::String |
◆ Super
|
private |
◆ TaskFactoryOP
Constructor & Destructor Documentation
◆ BDR() [1/2]
| protocols::forge::components::BDR::BDR | ( | ) |
default constructor
◆ BDR() [2/2]
◆ ~BDR()
|
overridedefault |
default destructor
Member Function Documentation
◆ add_instruction()
| void protocols::forge::components::BDR::add_instruction | ( | BuildInstructionOP | bi, |
| String const & | aa_during_design_refine = String() |
||
| ) |
add instruction to the manager of this BDR (no copy)
- Parameters
-
[in] bi BuildInstruction [in] aa_during_design_refine The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert [in] bi BuildInstruction [in] aa_during_design_refine The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly. Default empty string.
References protocols::forge::build::BuildManager::add(), design_info_, manager_, and vlb_.
◆ allowed_surface_aa()
|
staticprivate |
return a boolean vector specifying allowed a.a. when designing on the surface
References core::chemical::aa_from_oneletter_code().
Referenced by process_continuous_design_string(), and process_insert_design_string().
◆ apply()
|
overridevirtual |
apply defined moves to given Pose
Implements protocols::moves::Mover.
References centroid_build(), design_refine(), dr_cycles_, protocols::simple_filters::dssp(), protocols::moves::FAIL_DO_NOT_RETRY, core::chemical::modifications::FAIL_RETRY, protocols::moves::FAIL_RETRY, loops_buns_polar_calc_name(), manager_, core::pose::Pose::metric(), protocols::moves::MS_SUCCESS, neighborhood_buns_polar_calc_name(), neighborhood_calc_name(), protocols::moves::Mover::set_last_move_status(), and protocols::forge::build::BuildManager::union_of_intervals_containing_undefined_positions().
◆ centroid_build()
|
private |
run the centroid level build stage
- Returns
- true if loop closed, false otherwise
References centroid_loop_mover_str_, centroid_sfx_, core::scoring::Energies::clear(), protocols::forge::components::VLB_VallMemoryUsage::CLEAR_IF_CACHING_FRAGMENTS, protocols::denovo_design::construct_poly_ala_pose(), protocols::toolbox::pose_manipulation::construct_poly_ala_pose(), core::pose::Pose::energies(), core::chemical::FULL_ATOM_t, core::conformation::Residue::is_protein(), manager_, max_linear_chainbreak_, core::chemical::ResidueTypeBase::mode(), protocols::forge::build::BuildManager::modify(), protocols::moves::MS_SUCCESS, protocols::forge::build::BuildManager::original2modified(), core::pose::Pose::residue(), protocols::forge::methods::restore_residues(), core::pose::Pose::sequence(), core::pose::Pose::size(), core::util::switch_to_residue_type_set(), core::conformation::Residue::type(), use_fullmer_, use_sequence_bias_, and vlb_.
Referenced by apply().
◆ centroid_loop_mover_str() [1/2]
|
inline |
the loop mover string to use during centroid build (default "RemodelLoopMover")
- Remarks
- set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"
References centroid_loop_mover_str_.
◆ centroid_loop_mover_str() [2/2]
|
inline |
the loop mover string to use during centroid build
- Remarks
- set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"
References centroid_loop_mover_str_.
◆ centroid_scorefunction() [1/3]
| BDR::ScoreFunction const & protocols::forge::components::BDR::centroid_scorefunction | ( | ) | const |
the centroid level score function, default "remodel_cen"
References centroid_sfx_.
◆ centroid_scorefunction() [2/3]
| void protocols::forge::components::BDR::centroid_scorefunction | ( | ScoreFunction const & | sfx | ) |
set the centroid level score function
References centroid_sfx_, and core::scoring::ScoreFunction::clone().
◆ centroid_scorefunction() [3/3]
| void protocols::forge::components::BDR::centroid_scorefunction | ( | ScoreFunctionOP | sfx | ) |
set the centroid level score function
References centroid_sfx_.
◆ clone()
|
overridevirtual |
clone this object
Reimplemented from protocols::moves::Mover.
◆ create_directed_dependency()
| void protocols::forge::components::BDR::create_directed_dependency | ( | BuildInstructionOP | u, |
| BuildInstructionOP | v | ||
| ) |
create directed dependency between two instructions
References protocols::forge::build::BuildManager::create_directed_dependency(), manager_, and protocols::hybridization::u.
◆ design_refine()
|
private |
run the design-refine stage
- Returns
- currently always true
References protocols::cluster::calibur::aa, core::pose::annotated_to_oneletter_sequence(), core::scoring::Energies::clear(), design_info_, dr_cycles_, core::pose::Pose::energies(), core::pose::Pose::fold_tree(), protocols::forge::methods::fold_tree_from_loops(), fullatom_sfx_, generic_taskfactory(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::scoring::linear_chainbreak, protocols::forge::methods::linear_chainbreak(), manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap_as_OP(), neighborhood_calc_name(), protocols::forge::build::BuildManager::new_positions(), protocols::forge::build::BuildManager::original2modified_interval_endpoints(), process_continuous_design_string(), process_insert_design_string(), redesign_loop_neighborhood_, core::util::remove_cutpoint_variants(), protocols::loops::remove_cutpoint_variants(), core::pose::Pose::size(), and protocols::forge::components::TR().
Referenced by apply().
◆ dr_cycles() [1/2]
|
inline |
the number of design-refine cycles to perform, default 3
References dr_cycles_.
◆ dr_cycles() [2/2]
|
inline |
set the number of design-refine cycles to perform
- Remarks
- set this to 0 to skip design-refine
References dr_cycles_.
◆ fresh_instance()
|
overridevirtual |
create this type of object
Reimplemented from protocols::moves::Mover.
◆ fullatom_scorefunction() [1/3]
| BDR::ScoreFunction const & protocols::forge::components::BDR::fullatom_scorefunction | ( | ) | const |
the full-atom level score function, default score12
the full-atom level score function
References fullatom_sfx_.
◆ fullatom_scorefunction() [2/3]
| void protocols::forge::components::BDR::fullatom_scorefunction | ( | ScoreFunction const & | sfx | ) |
set the full-atom level score function
References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.
◆ fullatom_scorefunction() [3/3]
| void protocols::forge::components::BDR::fullatom_scorefunction | ( | ScoreFunctionOP | sfx | ) |
set the full-atom level score function
References fullatom_sfx_.
◆ generic_taskfactory()
|
private |
return a TaskFactory useable as a starting point for either design or refinement
References resfile_.
Referenced by design_refine().
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
◆ loops_buns_polar_calc_name()
|
inlinestatic |
the name for the loops' buried unsatisfied polars calculator
Referenced by apply().
◆ max_linear_chainbreak() [1/2]
|
inline |
the maximum allowed linear chainbreak (default 0.07)
References max_linear_chainbreak_.
◆ max_linear_chainbreak() [2/2]
|
inline |
the maximum allowed linear chainbreak
References max_linear_chainbreak_.
◆ neighborhood_buns_polar_calc_name()
|
inlinestatic |
the name for the loops' neighborhood buried unsatisfied polars calculator
Referenced by apply().
◆ neighborhood_calc_name()
|
inlinestatic |
the name for the loops' neighborhood calculator
Referenced by apply(), and design_refine().
◆ operator=()
copy assignment
- Remarks
- Mover base class prevents this from working properly...
◆ process_continuous_design_string()
|
private |
process a continuous design string, adding appropriate operations to the TaskFactory
References core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), and protocols::forge::build::Interval::left.
Referenced by design_refine().
◆ process_insert_design_string()
|
private |
process a design string containing an insert, adding appropriate operations to the TaskFactory
References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), allowed_surface_aa(), protocols::forge::build::Interval::left, protocols::forge::build::Interval::length(), and protocols::forge::build::Interval::right.
Referenced by design_refine().
◆ redesign_loop_neighborhood() [1/2]
|
inline |
redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)
References redesign_loop_neighborhood_.
◆ redesign_loop_neighborhood() [2/2]
|
inline |
redesign the neighborhood around the loop? if false, then just repacks during the design phase
References redesign_loop_neighborhood_.
◆ resfile() [1/2]
|
inline |
name of the resfile to use during design-refine; empty string implies no resfile
References resfile_.
◆ resfile() [2/2]
|
inline |
name of the resfile to use during design-refine; empty string implies no resfile
References protocols::abinitio::filename(), and resfile_.
◆ use_fullmer() [1/2]
|
inline |
use full-mer fragments when building the loop? (default false)
References use_fullmer_.
◆ use_fullmer() [2/2]
|
inline |
use full-mer fragments when building the loop?
References use_fullmer_.
◆ use_sequence_bias() [1/2]
|
inline |
use sequence biased fragments when building the loop? (default false)
References use_sequence_bias_.
◆ use_sequence_bias() [2/2]
|
inline |
use sequence biased fragments when building the loop? (default false)
References use_sequence_bias_.
Member Data Documentation
◆ centroid_loop_mover_str_
|
private |
the loop mover string to use during centroid build (default "RemodelLoopMover")
- Remarks
- set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"
Referenced by centroid_build(), and centroid_loop_mover_str().
◆ centroid_sfx_
|
private |
the centroid scorefunction to use, default "remodel_cen"
Referenced by centroid_build(), and centroid_scorefunction().
◆ design_info_
|
private |
Stores instructions' original interval and a string denoting the sequence during design.
- Remarks
- This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.
Referenced by add_instruction(), and design_refine().
◆ dr_cycles_
|
private |
the number of design-refine cycles to perform, default 3
Referenced by apply(), design_refine(), and dr_cycles().
◆ fullatom_sfx_
|
private |
the full-atom scorefunction to use, default score12
Referenced by design_refine(), and fullatom_scorefunction().
◆ manager_
|
private |
the BuildManager
Referenced by add_instruction(), apply(), centroid_build(), create_directed_dependency(), and design_refine().
◆ max_linear_chainbreak_
|
private |
the maximum allowed linear chainbreak (default 0.07)
Referenced by centroid_build(), design_refine(), and max_linear_chainbreak().
◆ redesign_loop_neighborhood_
|
private |
redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true)
Referenced by design_refine(), and redesign_loop_neighborhood().
◆ resfile_
|
private |
name of the resfile to use during design-refine; empty string implies no resfile
Referenced by generic_taskfactory(), and resfile().
◆ use_fullmer_
|
private |
use full-mer fragments when building the loop? (default false)
Referenced by centroid_build(), and use_fullmer().
◆ use_sequence_bias_
|
private |
use sequence biased fragments when building the loop? (default false)
Referenced by centroid_build(), and use_sequence_bias().
◆ vlb_
|
private |
VLB for centroid_build.
- Remarks
- Store it here instead of re-instantiation each centroid_build() call so fragment caching works.
- Warning
- Remember to set this to null if the BuildManager changes.
Referenced by add_instruction(), BDR(), and centroid_build().
The documentation for this class was generated from the following files:
